A quantitative analysis of secondary RNA structure using domination based parameters on trees

Background  

It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure.     

Climatic Stress during Stand Development Alters the Sign and Magnitude of Age-Related Growth Responses in a Subtropical Mountain Pine

The modification of typical age-related growth by environmental changes is poorly understood, In part because there is a lack of consensus at individual tree level regarding age-dependent growth responses to climate warming as stands develop. To increase our current understanding about how multiple drivers of environmental change can modify growth responses as trees age we used tree ring data of a mountain subtropical pine species along an altitudinal gradient covering more than 2,200 m of altitude. We applied mixed-linear models to determine how absolute and relative age-dependent growth varies depending on stand development; and to quantify the relative importance of tree age and climate on individual tree growth responses. Tree age was the most important factor for tree growth in models parameterised using data from all forest developmental stages. Contrastingly, the relationship found between tree age and growth became non-significant in models parameterised using data corresponding to mature stages. These results suggest that although absolute tree growth can continuously increase along tree size when trees reach maturity age had no effect on growth. Tree growth was strongly reduced under increased annual temperature, leading to more constant age-related growth responses. Furthermore, young trees were the most sensitive to reductions in relative growth rates, but absolute growth was strongly reduced under increased temperature in old trees. Our results help to reconcile previous contrasting findings of age-related growth responses at the individual tree level, suggesting that the sign and magnitude of age-related growth responses vary with stand development. The different responses found to climate for absolute and relative growth rates suggest that young trees are particularly vulnerable under warming climate, but reduced absolute growth in old trees could alter the species’ potential as a carbon sink in the future.     

Pine microsatellite markers allow roots and ectomycorrhizas to be linked to individual trees

Linking roots and ectomycorrhizas (EcM) to individual host trees in the field is required to test whether individual trees support different ectomycorrhizal communities. Here we describe a method that identifies the source of EcM roots by PCR of polymorphic pine nuclear microsatellite loci using fluorescently labelled primers and high-throughput fragment analysis. ITS-PCR can also be performed on the same EcM DNA extract for fungal identification. The method was tested on five neighbouring Scots pine (Pinus sylvestris var scotica) trees in native woodland. Successful host tree identification from DNA extracts of EcM root tips was achieved for 93% of all root fragments recovered from soil cores. It was estimated that each individual mature pine sampled was colonised by between 15 and 19 EcM fungi. The most abundant fungal species were found on all five trees, and within the constraints of the sampling scheme, no differences between trees in EcM fungal community structure or composition were detected.     

Changements de la structure du paysage et richesse spécifique des fragments forestiers dans le sud-est du Brésil

We used the Hallé and Oldeman's groups of the present and of the future, as obtained by an architectural analysis of trees, in order to test the hypothesis that the group of young (or potential) trees is more sensitive to parameters of present landscape structure than the group of old trees. The landscape structure and the tree species richness of 11 remnant forest fragments, located in the riparian corridor of the Jacaré-Pepira river (S.E. Brazil), were studied. The results showed that the tree species richness may not be linked to the landscape structure changes that have been occurring since 1962 (date of the oldest aerial photographs from the region). The studied communities are probably still responding to the main landscape structure changes that occurred during the second half of the 19th and the beginning of the 20th century as a consequence of the expansion of coffee plantations. Furthermore, the group of the future presented significant correlations with a greater number of landscape indices, confirming the initial hypothesis of greater sensitivity of the younger trees to the present landscape structure. It appears also that the richness of the group of the future is mainly affected by the present landscape structure while the richness of the group of the present results from interactions with present and past landscape structures.     

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

Estimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated - the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.     

Dynamic steady state of patch-mosaic tree size structure of a mixed dipterocarp forest regulated by local crowding

A patch age- and tree size-structured simulator was applied to demonstrate the landscape dynamics of a lowland mixed dipterocarp forest, using census data over a 3 year interval from two 1 ha plots in northern West Kalimantan, Indonesia (Western Borneo). Tree growth rate and recruitment rate were estimated as functions of tree size and local crowding. The effect of local crowding was assumed to be one-sided through light competition, where the basal area for all trees larger than a target tree inside the circle of 10 m radius around the target was employed as the index of crowding. Estimated parameters were similar between the two plots. Tree mortality was expressed by descending function of tree size with asymptotic mortality for large trees corresponding to the gap formation rate. One parameter specifying the survival of trees at gap formation, which was required for the landscape-level simulation of a shifting-gap mosaic, was left undetermined from plot census data. Through simulation, this parameter was estimated so as to best fit the observed among-patch variation in terms of local basal area. The overall time course of simulation and tree size structure were not sensitive to this parameter, suggesting that one-sided competition along the vertical forest profile is a stronger determinant of average forest structure than among-patch horizontal heterogeneity in this forest. Simulated dynamic steady state successfully reproduced the observed forest architecture in the gap-dynamic landscape. It took about 400 years for a vacant landscape to be replaced by a steady-state architecture of forest. Sensitivity analysis suggests that steady-state basal area and biomass are most sensitive to changing gap formation rate and intrinsic size growth rate.     

Partitioned likelihood support and the evaluation of data set conflict

In simultaneous analyses of multiple data partitions, the trees relevant when measuring support for a clade are the optimal tree, and the best tree lacking the clade (i.e., the most reasonable alternative). The parsimony-based method of partitioned branch support (PBS) "forces" each data set to arbitrate between the two relevant trees. This value is the amount each data set contributes to clade support in the combined analysis, and can be very different to support apparent in separate analyses. The approach used in PBS can also be employed in likelihood: a simultaneous analysis of all data retrieves the maximum likelihood tree, and the best tree without the clade of interest is also found. Each data set is fitted to the two trees and the log-likelihood difference calculated, giving "partitioned likelihood support" (PLS) for each data set. These calculations can be performed regardless of the complexity of the ML model adopted. The significance of PLS can be evaluated using a variety of resampling methods, such as the Kishino-Hasegawa test, the Shimodiara-Hasegawa test, or likelihood weights, although the appropriateness and assumptions of these tests remains debated.     

Bias and error in using survey records for ponderosa pine landscape restoration

Aim Public land survey records are commonly used to reconstruct historical forest structure over large landscapes. Reconstruction studies have been criticized for using absolute measures of forest attributes, such as density and basal area, because of potential selection bias by surveyors and unknown measurement error. Current methods to identify bias are based upon statistical techniques whose assumptions may be violated for survey data. Our goals were to identify and directly estimate common sources of bias and error, and to test the accuracy of statistical methods to identify them. Location Forests in the western USA: Mogollon Plateau, Arizona; Blue Mountains, Oregon; Front Range, Colorado. Methods We quantified both selection bias and measurement error for survey data in three ponderosa pine landscapes by directly comparing measurements of bearing trees in survey notes with remeasurements of bearing trees at survey corners (384 corners and 812 trees evaluated). Results Selection bias was low in all areas and there was little variability among surveyors. Surveyors selected the closest tree to the corner 95% to 98% of the time, and hence bias may have limited impacts on reconstruction studies. Bourdo’s methods were able to successfully detect presence or absence of bias most of the time, but do not measure the rate of bias. Recording and omission errors were common but highly variable among surveyors. Measurements for bearing trees made by surveyors were generally accurate. Most bearings were less than 5° in error and most distances were within 5% of our remeasurements. Many, but not all, surveyors in the western USA probably estimated diameter of bearing trees at stump height (0.3 m). These estimates deviated from reconstructed diameters by a mean absolute error of 7.0 to 10.6 cm. Main conclusions Direct comparison of survey data at relocated corners is the only method that can determine if bias and error are meaningful. Data from relocated trees show that biased selection of trees is not likely to be an important source of error. Many surveyor errors would have no impact on reconstruction studies, but omission errors have the potential to have a large impact on results. We suggest how to reduce potential errors through data screening.     

On the studies of marking behavior of brown bear in terms of tree diameter selectivity

Original data on the diameter of bear trees and trees in the stand were collected during the years 2002–2009 at the Upper Pechora and in the Western Sayan. The data were processed using the two-sample Student’s test and correlation analysis. Comparison was based on the published data on the thickness of bear trees. Brown bears use the trees 2 to 89 cm in diameter for marking. As a rule bear trees exceed the trees of the stand in the average diameter that proves that bears select trees with larger diameter for marking.     

A support vector machine based test for incongruence between sets of trees in tree space

ABSTRACT: BACKGROUND: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. RESULTS: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. CONCLUSIONS: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license.     

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

The reconstruction of phylogenetic history is predicated on being able to accurately establish hypotheses of character homology, which involves sequence alignment for studies based on molecular sequence data. In an empirical study investigating nucleotide sequence alignment, we inferred phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based on complete small-subunit rDNA sequences, using six different multiple-alignment procedures: manual alignment based on the secondary structure of the 18S rRNA molecule, and automated similarity-based alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM computer programs. Trees were constructed using neighboring-joining, weighted-parsimony, and maximum- likelihood methods. All of the multiple sequence alignment procedures yielded the same basic structure for the estimate of the phylogenetic relationship among the taxa, which presumably represents the underlying phylogenetic signal. However, the placement of many of the taxa was sensitive to the alignment procedure used; and the different alignments produced trees that were on average more dissimilar from each other than did the different tree-building methods used. The multiple alignments from the different procedures varied greatly in length, but aligned sequence length was not a good predictor of the similarity of the resulting phylogenetic trees. We also systematically varied the gap weights (the relative cost of inserting a new gap into a sequence or extending an already-existing gap) for the ClustalW program, and this produced alignments that were at least as different from each other as those produced by the different alignment algorithms. Furthermore, there was no combination of gap weights that produced the same tree as that from the structure alignment, in spite of the fact that many of the alignments were similar in length to the structure alignment. We also investigated the phylogenetic information content of the helical and nonhelical regions of the rDNA, and conclude that the helical regions are the most informative. We therefore conclude that many of the literature disagreements concerning the phylogeny of the Apicomplexa are probably based on differences in sequence alignment strategies rather than differences in data or tree-building methods.      

Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees within a Species: Molecular Variance Parsimony

We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.     

Constructing minimal ancestral recombination graphs.

By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of recombination events. In contrast to previously known methods, which yield only estimated lower bounds, our method of detecting recombination always gives the minimum number of recombination events if the right kind of rooted trees are used in our algorithm. A new lower bound can be defined if rooted trees with fewer constraints are used. As well as studying how often it actually is equal to the minimum, we test how this new lower bound performs in comparison to some other lower bounds. Our study indicates that the new lower bound is an improvement on earlier bounds. Also, using simulated data, we investigate how well our method can recover the actual site-specific evolutionary relationships. In the presence of recombination, using a single tree to describe the evolution of the entire locus clearly leads to lower average recovery percentages than does our method. Our study shows that recovering the actual local tree topologies can be done more accurately than estimating the actual number of recombination events.     

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

The desire to infer the evolutionary history of a group of species should be more viable now that a considerable amount of multilocus molecular data is available. However, the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree. Further, commonly used methods of combining data, such as the concatenation method, are known to be inconsistent in some circumstances. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions, such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a complete stochastic model to estimate gene trees, species trees, ancestral population sizes, and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus data sets of DNA sequences. The estimates of the species tree topology and divergence times appear to be robust to the prior of the population size, whereas the estimates of effective population sizes are sensitive to the prior used in the analysis. These analyses also suggest that the model is superior to the concatenation method in fitting these data sets and thus provides a more realistic assessment of the variability in the distribution of the species tree that may have produced the molecular information at hand. Future improvements of our model and algorithm should include consideration of other factors that can cause discordance of gene trees and species trees, such as horizontal transfer or gene duplication.     

Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life

Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.     

Phylogenetic analyses of amino acid variation in the serpin proteins

Phylogenetic analyses of 110 serpin protein sequences revealed clades consistent with independent phylogenetic analyses based on exon-intron structure and diagnostic amino acid sites. Trees were estimated by maximum likelihood, neighbor joining, and partial split decomposition using both the BLOSUM 62 and Jones-Taylor-Thornton substitution matrices. Neighbor-joining trees gave results closest to those based on independent analyses using genomic and chromosomal data. The maximum-likelihood trees derived using the quartet puzzling algorithm were very conservative, producing many small clades that separated groups of proteins that other results suggest were related. Independent analyses based on exon-intron structure suggested that a neighbor-joining tree was more accurate than maximum-likelihood trees obtained using the quartet puzzling algorithm.     

Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data

Alvarez, B., Crisp, M.D., Driver, F., Hooper, J.N.A. & Van Soest, R.W.M. (2000). Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data. —Zoologica Scripta, 29, 169–198. Twenty‐seven species of marine sponges belonging to Axinellidae and related groups (Halichondriidae, Dictyonellidae, Agelasida) were selected to test the monophyly of Axinellidae and investigate their phylogenetic relationships using parsimony and maximum likelihood methods. Partial 28S rDNA sequences, including the D3 domain, and traditional morphological characters (mainly skeletal ones) were used independently to construct phylogenetic trees. Sequences were aligned using the appropriate model of secondary structure of the RNA and compared to that produced by the multiple sequence alignment program, ClustalW. The alignment using secondary structure constraints produced a better estimate of the phylogeny and was demonstrated to be an effective and objective method. Results of the cladistic analyses of the molecular and morphological data sets were not fully congruent; the morphological data suggest that Axinellidae is monophyletic, however, the molecular data suggest that it is nonmonophyletic. The single most‐parsimonious tree derived from the molecular data showed that species of Axinella (except A. polypoides) are united in a clade that is more closely related to members of Agelasida than to other species of Axinellidae; the remaining members of Axinellidae form a monophyletic group that is closely related to the families Dictyonellidae and Halichondriidae. The consensus tree of 20 most‐parsimonious trees from the morphological analysis, on the other hand, showed that all the sampled species of Axinellidae belong to a monophyletic group which is closely related to the species of Dictyonellidae and Halichondriidae. Only two branches were identical in both cladograms, the one uniting the species of Ptilocaulis and Reniochalina and the one with the species of Dictyonellidae. The robustness of the molecular and morphological trees (or parts of the trees), was tested using bootstrap, jack‐knife, PTP and T‐PTP tests. The results of the PTP test were significant indicating significant cladistic structure in both data sets. The bootstrap and jack‐knife values indicate that the molecular tree is in general better supported than the morphological one. The lack of morphological characters and the homoplastic nature of some may explain the weak support of the morphological tree. A T‐PTP test of nonmonophyly showed that the nonmonophyly of Axinellidae, as indicated by the results of the molecular analysis, is not significant; however, a T‐PTP test of monophyly of Axinellidae, as indicated by the morphological tree, produced significant results. This indicates that the monophyly of Axinellidae based on morphological data cannot be rejected; the family however, cannot be defined in terms of a unique diagnostic character common to all members of the ingroup. Tests of heterogeneity (reciprocal T‐PTP and partition homogeneity test) indicated that the data partitions are heterogeneous, which could be due to sampling errors (in either data set) or differences in the underlying phylogenies; therefore data were not combined in a single analysis. Further, both data sets are unequally sized (95 informative molecular characters vs. 16 informative morphological characters), which means that the molecular signal could swamp the morphological signal if the data is combined. Nonmonophyly of Axinellidae is supported by chemical and genetic evidence available in the literature and DNA sequences data of axinellid species from New Zealand. However, this needs to be confirmed using independent evidence from different genes (or gene regions), biochemistry, histology or cell ultrastructure. Therefore, no changes to the taxonomic position of the family in the higher classification are proposed at this stage.     

Toward more meaningful hierarchical classification of protein three-dimensional structures.

Recently, several hierarchical classifications of protein three-dimensional (3D) structures have been published. However, none of them provides any assessment of the validity of a hierarchical representation or test individual clusters contained within. In fact, testing here of published trees reveals that they vary in meaning. Protein structure similarity measures are then assessed in terms of the robustness of the resulting trees for 24 protein families. A meaningful tree is defined as one in which all the clusters are found to be reliable according to a jackknife test. With the use of this criterion, a previously published similarity measure described as a "better RMS" is shown in fact to be usually less suited to protein fold classification than normal RMS after superposition. Here the "best" protein structure similarity measure for hierarchical classification-in terms of that which after clustering produces the highest number of meaningful trees, 20, for the 24 families-is found to be a new one. This measure includes information on the relationship of a distance at a given aligned position in a pair to the rest of the unique distances at that position in a protein family. There are only 2 families of the 24 tested, the globins (3 trees) and Kazal-type serine proteinase inhibitors (21 trees), in which the topology (branching order) of the meaningful 3D structure-based trees is constant. Thus, a new view of protein family sequence-structure relationships is afforded by comparing meaningful trees for each family. More generally, there is a need for care in interpretation of the results of those molecular biology algorithms that force a tree structure on data without assessing its applicability. Proteins 1999;37:20-29.     

A model to assess relationships between forest dynamics and spatial structure

Abstract. A spatially explicit model was developed to study the relationships between the dynamics and spatial structure of forest stands. The objective was to test whether tree spatial structure can be used as an indicator of stand dynamics. The model simulates the growth, mortality and recruitment of trees in a multi‐specific and uneven‐aged stand. It includes deterministic and stochastic processes so that repeated simulations do not lead to the same stand but provide several possible results for a given dynamic (defined by a set of parameters). Second‐order neighbourhood analyses were used to characterize the resulting spatial structures. They showed a high variability for a given set of parameters. Only the main trends in the spatial structure can be interpreted. Sensitivity analyses, concerning the influence of competition on spatial structure, showed that in heterogeneous stands confounding effects can hinder the interpretation of the spatial structure if all the trees are considered. The spatial structure of the canopy trees alone proved easier to interpret as it is directly linked to post recruitment competition. Inference on the dominant modality of competition (one‐sided or two‐sided) based on the spatial structure proved difficult.